ADP-ribosylation factors (ARFs) are a family of about 20-kDa guanine nucleotide- binding proteins that were originally identified by their ability to stimulate in vitro cholera toxin-catalyzed ADP-ribosylation of Gsalpha, the alpha subunit of the stimulatory heterotrimeric GTP-binding protein of the adenylyl cyclase system. More recently, ARFs have been implicated in intracellular protein trafficking and are thought to be involved in the assembly of non-clathrin coated vesicles. Based on molecular cloning, at least six mammalian ARFs are known. These fall into three classes based on deduced amino acid sequence, size, and phylogenetic analysis. Characterization of the human genes encoding ARFs 4 and 5 indicate that the gene structure is conserved. The locations of the introns within the coding regions of the genes are identical. Consistent with the notion that ARFs 4 and 5 belong to a separate class, the locations of introns differ from those of the class I ARF genes (ARFs 1, 2 and 3). As an exception to this observation, the introns that disrupt the coding region to form the exon encoding the sequence DVGG, which forms the DXXG consensus sequence that has been proposed to coordinate binding to Mg2+ and the beta phosphate of GDP, are located in identical positions in the class I and II ARFs. In contrast to the gene structure of the class I ARFs, where intron 4 divides the NKXD consensus sequence between exons 4 and 5, the class II ARF genes do not have an intron dividing this consensus sequence. This organization of the functional domains of the ARF proteins into separate exons is similar to other GTP-binding protein genes (e.g., Gsalpha, N-ras).